#|
library(bibtex)
library(openalexR)Thank you for using openalexR!
To acknowledge our work, please cite the package by calling
`citation("openalexR")`.library(writexl)
# library(dplyr)
# library(ggplot2)
# library(knitr)
kp <- bibtex::read.bib("./key-paper.bib")
dois <- sapply(
kp,
function(x) {
x$doi
}
)#|
library(ggraph)Loading required package: ggplot2library(tidygraph)
Attaching package: 'tidygraph'The following object is masked from 'package:stats':
filterkey_works <- oa_fetch(
entity = "works",
doi = dois,
verbose = FALSE
)
ids <- openalexR:::shorten_oaid(key_works$id)
citing_kp <- lapply(
ids,
function(id) {
oa_fetch(
entity = "works",
output = "tibble",
cites = id,
verbose = FALSE
)
}
)Warning in oa_fetch(entity = "works", output = "tibble", cites = id, verbose =
FALSE): No collection found!names(citing_kp) <- ids
cited_by_kp <- lapply(
ids,
function(id) {
oa_fetch(
entity = "works",
output = "tibble",
cited_by = id,
verbose = FALSE
)
}
)
names(cited_by_kp) <- ids
if (file.exists("snowball.rds")) {
snowball <- readRDS("snowball.rds")
} else {
snowball <- oa_snowball(
identifier = ids,
verbose = FALSE
)
saveRDS(snowball, "snowball.rds")
}
flat_snow <- snowball2df(snowball) |>
as_tibble()snowball_excel.xlsx)###
no_edges <- snowball$edges |>
unlist() |>
table() |>
sort() |>
as.data.frame() |>
rename(
no_connections = Freq,
id = Var1
)
###
no_referenced_works <- sapply(
snowball$node["referenced_works"][[1]],
length
)
no_referenced_works <- data.frame(
id = snowball$node["id"],
no_referenced_works = no_referenced_works
)
###
citations_per_year <- flat_snow |>
select(
id,
publication_year,
cited_by_count
) |>
mutate(
years_published = 2023 - publication_year
) |>
mutate(
avg_citations_per_year = cited_by_count / years_published
) |>
arrange(desc(cited_by_count)) |>
select(
id,
avg_citations_per_year
) |>
rename(cited_global_per_year = avg_citations_per_year)
###
export <- flat_snow |>
select(
id,
publication_year,
display_name,
doi,
cited_by_count,
ab
) |>
rename(
cited_global = cited_by_count,
title = display_name,
abstract = ab
)
export$author <- sapply(
flat_snow$author,
function(z) {
paste(unlist(z["au_display_name"]), collapse = ", ")
}
)
export$author_institute <- sapply(
flat_snow$author,
function(z) {
paste(unlist(z["institution_display_name"]), collapse = ", ")
}
)
export$institute_country <- sapply(
flat_snow$author,
function(z) {
paste(unlist(z["institution_country_code"]), collapse = ", ")
}
)
concepts <- lapply(
flat_snow$concepts,
function(x){
x |>
select(level, display_name, score)
}
)
export$concepts_l0 <- sapply(
concepts,
function(x) {
x |>
filter(level == 0) |>
mutate(name = paste0(display_name, " (", round(score, digits = 3), ")")) |>
select(name) |>
unlist() |>
paste0(collapse = ", ")
}
)
export$concepts_l1 <- sapply(
concepts,
function(x) {
x |>
filter(level == 1) |>
mutate(name = paste0(display_name, " (", round(score, digits = 3), ")")) |>
select(name) |>
unlist() |>
paste0(collapse = ", ")
}
)
export$concepts_l2 <- sapply(
concepts,
function(x) {
x |>
filter(level == 2) |>
mutate(name = paste0(display_name, " (", round(score, digits = 3), ")")) |>
select(name) |>
unlist() |>
paste0(collapse = ", ")
}
)
export$concepts_l3 <- sapply(
concepts,
function(x) {
x |>
filter(level == 3) |>
mutate(name = paste0(display_name, " (", round(score, digits = 3), ")")) |>
select(name) |>
unlist() |>
paste0(collapse = ", ")
}
)
export$concepts_l4 <- sapply(
concepts,
function(x) {
x |>
filter(level == 4) |>
mutate(name = paste0(display_name, " (", round(score, digits = 3), ")")) |>
select(name) |>
unlist() |>
paste0(collapse = ", ")
}
)
export$concepts_l5 <- sapply(
concepts,
function(x) {
x |>
filter(level == 5) |>
mutate(name = paste0(display_name, " (", round(score, digits = 3), ")")) |>
select(name) |>
unlist() |>
paste0(collapse = ", ")
}
)
xlsx <- export |>
full_join(no_edges, by = "id") |>
full_join(no_referenced_works, by = "id") |>
full_join(citations_per_year, by = "id") |>
dplyr::relocate(author, .after = id) |>
arrange(desc(cited_global))
la <- xlsx$abstract |>
nchar() >= 3000
xlsx$abstract[la] <- substr(xlsx$abstract[la], 1, 3000)
xlsx |>
dplyr::relocate(cited_global_per_year, .after = cited_global) |>
dplyr::relocate(no_referenced_works, .after = doi) |>
dplyr::relocate(no_connections, .before = abstract) |>
dplyr::relocate(concepts_l0, .before = abstract) |>
dplyr::relocate(concepts_l1, .before = abstract) |>
dplyr::relocate(concepts_l2, .before = abstract) |>
dplyr::relocate(concepts_l3, .before = abstract) |>
dplyr::relocate(concepts_l4, .before = abstract) |>
dplyr::relocate(concepts_l5, .before = abstract) |>
dplyr::relocate(author_institute, .before = abstract) |>
dplyr::relocate(institute_country, .before = abstract) |>
writexl::write_xlsx(file.path(".", "data", "snowball_excel.xlsx"))#|
snowball$nodes$cited_by_count_by_year <- snowball$nodes$cited_by_count / (2024 - snowball$nodes$publication_year)
### Size cited_by_count_by_year
p_cby <- snowball |>
as_tbl_graph() |>
ggraph(graph = , layout = "stress") +
geom_edge_link(aes(alpha = after_stat(index)), show.legend = FALSE) +
geom_node_point(aes(fill = oa_input, size = cited_by_count_by_year), shape = 21, color = "white") +
geom_node_label(aes(filter = oa_input, label = id), nudge_y = 0.2, size = 3) +
scale_edge_width(range = c(0.1, 1.5), guide = "none") +
scale_size(range = c(3, 10), guide = "none") +
scale_fill_manual(values = c("#a3ad62", "#d46780"), na.value = "grey", name = "") +
theme_graph() +
theme(
plot.background = element_rect(fill = "transparent", colour = NA),
panel.background = element_rect(fill = "transparent", colour = NA),
legend.position = "bottom"
) +
guides(fill = "none") +
ggtitle("Cited by average count per year")
ggsave("cited_by_count_by_year.pdf", plot = p_cby, device = cairo_pdf, width = 20, height = 15)Warning: Using the `size` aesthetic in this geom was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` in the `default_aes` field and elsewhere instead.ggsave("cited_by_count_by_year.png", plot = p_cby, width = 20, height = 15, bg = "white")
### Size cited_by_count
p_cb <- snowball |>
as_tbl_graph() |>
ggraph(graph = , layout = "stress") +
geom_edge_link(aes(alpha = after_stat(index)), show.legend = FALSE) +
geom_node_point(aes(fill = oa_input, size = cited_by_count), shape = 21, color = "white") +
geom_node_label(aes(filter = oa_input, label = id), nudge_y = 0.2, size = 3) +
scale_edge_width(range = c(0.1, 1.5), guide = "none") +
scale_size(range = c(3, 10), guide = "none") +
scale_fill_manual(values = c("#a3ad62", "#d46780"), na.value = "grey", name = "") +
theme_graph() +
theme(
plot.background = element_rect(fill = "transparent", colour = NA),
panel.background = element_rect(fill = "transparent", colour = NA),
legend.position = "bottom"
) +
guides(fill = "none") +
ggtitle("Cited by count")
ggsave("cited_by_count.pdf", plot = p_cb, device = cairo_pdf, width = 20, height = 15)
ggsave("cited_by_count.png", plot = p_cb, width = 20, height = 15, bg = "white")